Spontaneous mutations in hlyD and tuf genes result in resistance of Dickeya solani IPO 2222 to phage ϕD5 but cause decreased bacterial fitness and virulence in planta

Abstract

Lytic bacteriophages able to infect and kill Dickeya spp. can be readily isolated from virtually all Dickeya spp. containing environments, yet little is known about the selective pressure those viruses exert on their hosts. Two spontaneous D. solani IPO 2222 mutants (0.8% of all obtained mutants), DsR34 and DsR207, resistant to infection caused by lytic phage vB_Dsol_D5 (ΦD5) were identified in this study that expressed a reduced ability to macerate potato tuber tissues compared to the wild-type, phage-susceptible D. solani IPO 2222 strain. Genome sequencing revealed that genes encoding: secretion protein HlyD (in mutant DsR34) and elongation factor Tu (EF-Tu) (in mutant DsR207) were altered in these strains. These mutations impacted the DsR34 and DsR207 proteomes. Features essential for the ecological success of these mutants in a plant environment, including their ability to use various carbon and nitrogen sources, production of plant cell wall degrading enzymes, ability to form biofilms, siderophore production, swimming and swarming motility and virulence in planta were assessed. Compared to the wild-type strain, D. solani IPO 2222, mutants DsR34 and DsR207 had a reduced ability to macerate chicory leaves and to colonize and cause symptoms in growing potato plants.

Adaptive loss of tRNA gene expression leads to phage resistance in a marineSynechococcuscyanobacterium

“…The most well-known passive resistance mechanisms in bacteria arise from changes in an outer cellular component that phages use as receptors, thus preventing phage adsorption and entry into the cell 6,[7][8][9][10][11] , and thus function extracellularly. Intracellular mutations or loss-offunction of cellular components as a means of resistance is rarely reported in bacteria, but based on our findings, may be more common than currently appreciated.…”

“…Loss of function, or "passive" resistance mechanisms, can also result in resistance to phage infection. The most well studied examples of this latter type of resistance are mutations that lead to changes in the cell wall, for example, alterations in receptors that impact phage adsorption [7][8][9][10][11] , or loss of extracellular polymers needed for adsorption 12,13 . Intracellular resistance caused by a loss of function has been less well studied.…”

Soft rot pathogen Dickeya dadantii 3937 produces tailocins resembling the tails of Peduovirus P2

“…For the AFM analysis, purified and PEG-concentrated particles were used directly without further preparations. AFM imaging was conducted in air mode using the Bioscope Resolve microscope (Bruker), in ScanAsyst (Peak Force Tapping) mode, employing the SCANASYST-AIR probes (f0 7.0 kHz, diameter < 12 nm, k: 0.4 N/m) as described earlier ( Sokolova et al, 2023 ). Similarly, as described for TEM analysis, for AFM, at least 10 images were taken for each preparation to estimate the diameters of the particles.…”

Soft rot pathogenDickeya dadantii3937 produces tailocins resembling the tails ofEnterobacteriabacteriophage P2

“…For the AFM analysis, purified and PEG-concentrated particles were used directly without further preparations. AFM imaging was conducted in air mode using the Bioscope Resolve microscope (Bruker), in ScanAsyst (Peak Force Tapping) mode, employing the SCANASYST-AIR probes (f0 7.0 kHz, diameter <12 nm, k: 0.4 N/m) as described earlier (62). Similarly, as described for TEM analysis, for AFM, at least ten images were taken for each preparation to estimate the diameters of the particles.…”